It seems that when an answer is implicitly deleted along with the parent question, it loses its checkmark. This, coupled with the fact that the timeline view is broken for deleted questions, makes it impossible to tell what the accepted answer to a deleted question used to be.

If, on the other hand, only the accepted answer is deleted, it retains the checkmark.

I recently had an old question deleted, and neither the +2 rep to me or the +15 rep to the answerer (9 upvotes + accept) were revoked, so it looks like the answer is still technically accepted.